Several documents are currently available:

• New: Documentation is getting reformatted into sphinx/rst format and hosted at readthedocs. Note that the conversion from the old manual is currently under way so that this new document is not yet complete. But a new section "Contributing" has been added.
  
  
• The old format final online documentation
  
  
• Our on-line code browser provides a view of the various subroutines, functions and variables, showing how they are called and used.
  
  

And just for reference:

• The old Release-1 online documentation
  
  
• An old MITgcm "Developer's HOWTO" document is available in html or as PDF file
  
  
• The old online code browser
  
  

Papers charting the development of MITgcm can be found here.